def pims_transform_anime(global_config: dict, video_config: dict, video):
""" Apply transformations to an anime video, using pims pipelines. """
video = preprocess_anime(global_config, video_config, video)
trans = [pims.pipeline(lambda img: resize(img, (ANIME_SIZE, ANIME_SIZE))),
pims.pipeline(skimage.img_as_ubyte)
]
return transform(trans, video)
def test_composed_pipelines(self):
color_channel = pims.pipeline(_color_channel)
rescale = pims.pipeline(_rescale)
composed = rescale(color_channel(self.v, 0))
expected = _rescale(_color_channel(self.v[0], 0))
assert_image_equal(composed[0], expected)
def test_composed_pipelines(self):
color_channel = pims.pipeline(_color_channel)
rescale = pims.pipeline(_rescale)
composed = rescale(color_channel(self.v, 0))
expected = _rescale(_color_channel(self.v[0], 0))
assert_image_equal(composed[0], expected)
def processVideo(videoPath, outputFolder, shape='circle'):
"""
Pipeline containing function to trim, mask and crop a video (provided by the process.csv file)
shape: 'circle' or 'polygon'
"""
print('processVideo called with: ', videoPath, outputFolder)
outputFilename = os.path.join(
outputFolder,
os.path.split(videoPath)[-1].strip(".mp4") + "_processed.mp4")
if os.path.exists(outputFilename):
print(outputFilename, "already exists. Terminating!")
return None
# get the required data from the process.csv file
df = pd.read_csv(os.path.join(os.path.split(videoPath)[0], "process.csv"),
index_col=0)
start = df.loc[os.path.split(videoPath)[-1], 'start']
end = df.loc[os.path.split(videoPath)[-1], 'end']
# Shorten processed videos to 1h
if end - start > 3600:
end = 3600 + start
if shape == 'circle':
circle = literal_eval(df.loc[os.path.split(videoPath)[-1], 'circle'])
# elif shape == 'polygon':
# vertices = np.array(literal_eval(df.loc[os.path.split(videoPath)[-1], 'vertices']))
crop = literal_eval(df.loc[os.path.split(videoPath)[-1], 'crop'])
video = pims.ImageIOReader(videoPath)
fps = video.frame_rate
# pipelines
# masking pipeline
masking_pipeline = pims.pipeline(maskFrame_circle)
masking_kwargs = dict(circle=circle)
masked_video = masking_pipeline(video, **masking_kwargs)
# cropping pipeline
cropping_pipeline = pims.pipeline(crop_frame)
cropping_kwargs = dict(crop=crop)
cropped_video = cropping_pipeline(masked_video, **cropping_kwargs)
# writing to disk
try:
os.mkdir(outputFolder)
except OSError:
print(
outputFolder,
"already exists! Continuing with the process without creating it.")
start_frame = int(start * fps)
end_frame = int(end * fps)
imageio.mimwrite(outputFilename,
cropped_video[start_frame:end_frame],
fps=fps)
print('Completed: processVideo with parameters: ', videoPath, outputFolder)
def maskVideo_rect(videoPath, outputFolder, reader='ImageIO'):
"""Function containing a pipeline which masks a desired ROI in a given video (provided by the maskROIs.csv file)
and saves the result"""
# get the maskCoords from the csv file
df = pd.read_csv(os.path.join(os.path.split(videoPath)[0], "maskROIs.csv"),
index_col=0)
maskCoords = tuple(df.loc[os.path.split(videoPath)[-1]])
# reader
if reader == 'ImageIO':
video = pims.ImageIOReader(videoPath)
elif reader == 'PyAV':
video = pims.Video(videoPath)
fps = video.frame_rate
# pipeline
r = maskCoords
masking_pipeline = pims.pipeline(maskFrame_rect)
kwargs = dict(maskCoords=r)
processed_video = masking_pipeline(video, **kwargs)
# writing to disk
try:
os.mkdir(outputFolder)
except OSError:
print(
outputFolder,
"already exists! Continuing with the process without creating it.")
outputFilename = os.path.join(
outputFolder,
os.path.split(videoPath)[-1].strip(".mp4") + "_masked.mp4")
imageio.mimwrite(outputFilename, processed_video, fps=fps)
def get_frames(file_path, frames, gaussian_filter_width=None, roi = None):
"""
opens the video and returns the requested frames as numpy array
Args:
file_path: path to video file
frames: integer or list of integers of the frames to be returned
gaussian_filter_width: if not None apply Gaussian filter
roi: region of interest, this allows to limit the search to a region of interest with the frame, the structure is
roi = [roi_center, roi_dimension], where
roi_center = [ro, co], roi_dimension = [h, w], where
ro, co is the center of the roi (row, columns) and
w, h is the width and the height of the roi
Note that roi dimensions w, h should be odd numbers!
"""
images = []
if not hasattr(frames, '__len__'):
frames = [frames]
if not roi is None:
[roi_center, roi_dimension] = roi
v = pims.Video(file_path)
video = rgb2gray_pipeline(v)
if not gaussian_filter_width is None:
gaussian_filter_pipeline = pipeline(gaussian_filter)
video = gaussian_filter_pipeline(video, gaussian_filter_width)
frame_shape = np.shape(video[frames[0]])
for frame in frames:
image = video[frame]
# reduce image to roi
if not roi is None:
[roi_center, roi_dimension] = roi
image_roi = image[
int(roi_center[0] - (roi_dimension[0] - 1) / 2): int(
roi_center[0] + (roi_dimension[0] + 1) / 2),
int(roi_center[1] - (roi_dimension[1] - 1) / 2): int(roi_center[1] + (roi_dimension[1] + 1) / 2)
]
else:
image_roi = image
images.append(image_roi)
return images
def test_pipeline_with_args(self):
color_channel = pims.pipeline(_color_channel)
red = color_channel(self.v, 0)
green = color_channel(self.v, 1)
assert_image_equal(red[0], _color_channel(self.frame0, 0))
assert_image_equal(green[0], _color_channel(self.frame0, 1))
# Multiple pipelines backed by the same data are indep,
# so this call to red is unaffected by green above.
assert_image_equal(red[0], _color_channel(self.frame0, 0))
def test_pipeline_with_args(self):
color_channel = pims.pipeline(_color_channel)
red = color_channel(self.v, 0)
green = color_channel(self.v, 1)
assert_image_equal(red[0], _color_channel(self.frame0, 0))
assert_image_equal(green[0], _color_channel(self.frame0, 1))
# Multiple pipelines backed by the same data are indep,
# so this call to red is unaffected by green above.
assert_image_equal(red[0], _color_channel(self.frame0, 0))
def transform_manga(config: dict, frames):
""" Apply transformations to a sequence of manga pages. """
# crop whitespace from the edges
# top, bottom, left, right, color things
box = config["crop"]
trans = [lambda frames: pims.process.crop(frames,
((box[0], box[1]), (box[2], box[3]), (0, 0))),
# apply greyscale transformation
pims.as_grey,
# resize images
pims.pipeline(lambda img: resize(img, (MANGA_SIZE, MANGA_SIZE))),
to_ubyte
]
return transform(trans, frames)
def export_video(self, filename=None, rate=None, **kwargs):
"""For a list of kwargs, see pims.export"""
# TODO Save the canvas instead of the reader (including annotations)
presets = dict(avi=dict(codec='libx264', quality=23),
mp4=dict(codec='mpeg4', quality=5),
mov=dict(codec='mpeg4', quality=5),
wmv=dict(codec='wmv2', quality=0.005))
str_filter = ";;".join(['All files (*.*)',
'H264 video (*.avi)',
'MPEG4 video (*.mp4 *.mov)',
'Windows Media Player video (*.wmv)'])
if filename is None:
try:
cur_dir = os.path.dirname(self.reader.filename)
except AttributeError:
cur_dir = ''
filename = QtWidgets.QFileDialog.getSaveFileName(self,
"Export Movie",
cur_dir,
str_filter)
if isinstance(filename, tuple):
# Handle discrepancy between PyQt4 and PySide APIs.
filename = filename[0]
ext = os.path.splitext(filename)[-1]
if ext[0] == '.':
ext = ext[1:]
try:
_kwargs = presets[ext]
except KeyError:
raise ValueError("Extension '.{}' is not a known format.".format(ext))
_kwargs.update(kwargs)
if rate is None:
try:
rate = float(self.reader.frame_rate)
except AttributeError or ValueError:
rate = 25.
self.reader.iter_axes = 't'
self.status = 'Saving to {}'.format(filename)
# PIMS v0.4 export() has a bug having to do with float precision
# fix that here using limit_denominator() from fractions
export(pipeline(to_rgb_uint8)(self.reader, autoscale=self.autoscale, force_color=self.force_color), filename,
Fraction(rate).limit_denominator(66535), **kwargs)
self.status = 'Done saving {}'.format(filename)
def test_pipeline_simple(self):
rescale = pims.pipeline(_rescale)
rescaled_v = rescale(self.v[:1])
assert_image_equal(rescaled_v[0], _rescale(self.frame0))
def test_pipeline_simple(self):
rescale = pims.pipeline(_rescale)
rescaled_v = rescale(self.v[:1])
assert_image_equal(rescaled_v[0], _rescale(self.frame0))
def extract_motion(filepath, target_path=None, gaussian_filter_width=2, use_trackpy =False, show_progress = True,
trackpy_parameters = None, min_frames = 0, max_frames = None, roi = None, dynamic_roi = False, center_of_mass=False):
"""
Takes in a bead video, and saves the bead's extracted position in every frame in a csv, and
(optionally) an uncorrupted version of the video
filepath: path to an avi file of the bead
target_path: (optional) if None same as video path
gaussian_filter_width: width (in pixels) of the gaussian used to smooth the video
use_trackpy: if True use Trackpy to better localize the brightest point, need to provid trackpy_parameters
show_progress: if True show progress (use when called from ipython notebook)
trackpy_parameters: parameters for trackpy (only needed if use_trackpy is True)
min_frames: first frame to analyze, usefull for debugging, if start from first frame
max_frames: max number of frames to analyze, usefull for debugging, if none do entire video
roi: region of interest, this allows to limit the search to a region of interest with the frame, the structure is
roi = [roi_center, roi_dimension], where
roi_center = [ro, co], roi_dimension = [h, w], where
ro, co is the center of the roi (row, columns) and
w, h is the width and the height of the roi
Note that roi dimensions w, h should be odd numbers!
Note that the order of the dimensions is vertical, horizontal, that is NOT x,y!
dynamic_roi: if True, dynamically track the roi, ie. the center of the roi of the next frame is the detected position of the currenrt frame. If false the roi is static
center_of_mass: calculate the position from the center of mass
returns: path to .csv file
"""
if target_path is None:
target_path = os.path.dirname(filepath)
assert os.path.isdir(target_path)
if use_trackpy:
assert 'diameter' in trackpy_parameters
if not 'minmass' in trackpy_parameters:
trackpy_parameters['minmass'] = None
trackpy_parameters['missing_frames'] = []
target_filename = os.path.join(target_path, os.path.basename(filepath).replace('.avi', '_data_globalmax.csv'))
v = pims.Video(filepath)
processed_v = rgb2gray_pipeline(v)
gaussian_filter_pipeline = pipeline(gaussian_filter)
filtered = gaussian_filter_pipeline(processed_v, gaussian_filter_width)
if max_frames is None:
max_frames=len(filtered)
else:
# make sure max_frames is integer
max_frames =int(max_frames)
if show_progress:
f = FloatProgress(min=min_frames, max=max_frames) # instantiate the bar
display(f) # display the bar
start_time = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')
print('start time:\t{:s}'.format(start_time))
image_size = np.shape(filtered[0]) # size of image
# find the maximum brightness pixel for every frame, corresponding to some consistent point at the bead
max_coors = []
skipped_frames_idx = []
if not roi is None:
[roi_center, roi_dimension] = roi
for i in [0, 1]:
# assert that roi fits in the image
assert roi_center[i] + (roi_dimension[i]+1) / 2 <= image_size[i]
assert roi_center[i] - (roi_dimension[i]+1) / 2 >= 0
# assert that roi_dimension are odd
assert roi_dimension[i] % 2 == 1
cols = ['y bright', 'x bright']
if center_of_mass:
cols = cols + ['x com', 'y com']
if use_trackpy:
cols = cols + ['x tp', 'y tp']
# we use range in this loop so that we can catch the CannotReadFrameError in the line where we try to access the next image
for index in range(min_frames, max_frames):
try:
image = filtered[index]
except CannotReadFrameError:
skipped_frames_idx.append(index)
po, roi = get_position(image, roi, dynamic_roi=dynamic_roi, center_of_mass=center_of_mass, use_trackpy=use_trackpy,
trackpy_parameters=trackpy_parameters)
if po is None:
trackpy_parameters['missing_frames'].append(index)
else:
max_coors.append(po)
if index % 1000 == 0:
if show_progress:
f.value += 1000
if not max_frames is None:
if index>max_frames:
break
df = pd.DataFrame(max_coors, columns=cols)
df.to_csv(target_filename)
end_time = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')
print('end time:\t{:s}'.format(end_time))
print('file written to:\n{:s}'.format(target_filename))
info = {
'filename_xy_position': target_filename,
'image_size':np.shape(filtered[0]),
'gaussian_filter_width':gaussian_filter_width,
'N_frames':len(filtered),
'use_trackpy':use_trackpy,
'center_of_mass':center_of_mass,
'start_time':start_time,
'end_time':end_time,
'max_frames':max_frames,
'skipped_frames_idx':skipped_frames_idx,
'N_skipped_frames': len(skipped_frames_idx),
'roi' : roi
}
# convert time back to datetime so that we can calculate the duration
start_time = datetime.datetime.strptime(start_time, '%Y-%m-%d %H:%M:%S')
end_time = datetime.datetime.strptime(end_time, '%Y-%m-%d %H:%M:%S')
info['extract. duration (min)'] = (end_time - start_time).seconds / 60
if use_trackpy:
info.update({
'trackpy_parameters': trackpy_parameters
})
if info['N_skipped_frames']>100:
print('WARNING: more than 100 frames corrupted in this video!!')
return info
import numpy as np import pandas as pd import os import matplotlib.pyplot as plt import scipy.optimize as sopt import glob from tqdm import tqdm import pims from pims import pipeline from skimage.color import rgb2gray rgb2gray_pipeline = pipeline(rgb2gray) from scipy.ndimage.filters import gaussian_filter from scipy.ndimage.measurements import center_of_mass import trackpy as tp # status bar from IPython.display import display from imageio.core import CannotReadFrameError import datetime import yaml import sys import subprocess
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import scipy.optimize as sopt
import pims
import scipy.spatial
import scipy.ndimage
from collections import Counter
import glob
import trackpy as tp
from pims import pipeline
from skimage.color import rgb2gray
rgb2gray_pipeline = pipeline(rgb2gray)
from joblib import Parallel, delayed
import multiprocessing
num_cores = multiprocessing.cpu_count()
def get_maxcoors(image, image_size):
pixel_max = np.argmax(image)
return(pixel_max%image_size, pixel_max/image_size)
def get_maxcoors_array(image_array, image_size):
maxes = []
for image in image_array:
pixel_max = np.argmax(image)